R devel - Jun 2018 - Bug 16719: kruskal.test documentation for formula

I submit a couple options for addressing bug 16719: kruskal.test
documentation for formula.
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16719

disallow-character.diff changes the documentation and error message
to indicate that factors are accepted.

allow-character.diff changes the kruskal.test functions to convert
character vectors to factors; documentation is updated accordingly.

I tested the updated functions with the examples in example.R. It is
based on the examples in the bug report.

If there is interest in applying either patch, especially the latter,
I want first to test the change on lots of existing programs that call
kruskal.test, to see if it causes any regressions. Is there a good place
to look for programs that use particular R functions?

I am having trouble building R, so I have so far tested these changes
only by patching revision 74631 (SVN head) and sourcing the resulting
kruskal.test.R in R 3.4.1 on OpenBSD 6.2. I thus have not tested the
R documentation files.

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Thomas Levine writes:
> I submit a couple options for addressing bug 16719: kruskal.test
> documentation for formula.
> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16719
>
> disallow-character.diff changes the documentation and error message
> to indicate that factors are accepted.
>
> allow-character.diff changes the kruskal.test functions to convert
> character vectors to factors; documentation is updated accordingly.
>
> I tested the updated functions with the examples in example.R. It is
> based on the examples in the bug report.
>
> If there is interest in applying either patch, especially the latter,
> I want first to test the change on lots of existing programs that call
> kruskal.test, to see if it causes any regressions. Is there a good place
> to look for programs that use particular R functions?
>
> I am having trouble building R, so I have so far tested these changes
> only by patching revision 74631 (SVN head) and sourcing the resulting
> kruskal.test.R in R 3.4.1 on OpenBSD 6.2. I thus have not tested the
> R documentation files.
I thought it was important to test the changes on lots of existing
programs that call kruskal.test, to see if it causes any regressions.

CRAN testing
------------
I downloaded all CRAN packages and checked whether they contained the
fixed expression "kruskal.test". (See "Makefile" and
"all-kruskal.r".)

I subsequently tested on all packages in CRAN that mentioned
"kruskal.test".

I patched the development version of R and built like this.

  ./configure --without-recommended-packages
  gmake
  cd src/library
  gmake all docs Rdfiles

This command was helpful for cleaning the repository tree.

  svn status | sed -n 's/^\?  *//p' | xargs rm -r

I tested three versions of kruskal.test

* SVN checkout 74844 with no modifications
* SVN checkout 74844 with disallow-character patch
* SVN checkout 74844 with allow-character patch

The test is to run all of the examples from all of the packages that
mention kruskal.test; with each example I ran, I recorded whether an
error was raised.  I ran all examples, regardless of whether the example
mentioned kruskal.test.  I compared the raising of an error among the
three builds of R/kruskal.test.

I ran these commands for each R version to build R, install the packages
referencing kruskal.test, and run the tests in parallel. The procedure
is available here; see the Makefile for more detail.
https://thomaslevine.com/scm/r-patches/dir?ci=6ea0db4fde&name=kruskal.test-numeric/testing

Run it with like this if you are so inclined.

  make -j 3 install
  make -j 3 test

I found 100 packages that referenced kruskal.test. (This was based on a
very crude string matching; some of these packages mentioned
kruskal.test only in the documentation.) Of these 100 packages, I was
able to install 39. I ran all of the examples in all of these packages,
a total of 2361 examples.

The successes and failures matched exactly among the three builds.
341 examples succeeded, and 2020 failed.
https://thomaslevine.com/scm/r-patches/artifact/5df57add4414970a

This is of course a lot of failures and a small proportion of the
packages. I only installed the packages whose dependencies were easy
for me to install (on OpenBSD 6.2), and some of those implicitly
depended on other things that were not available; this explains
all of the examples that raised errors.

Review of r-help
----------------
I also began to collect all kruskal.test calls that I could find in the
r-help archives. Formatting them to be appropriate for evaluation is
quite tedious, so I doubt I will follow through with this, but all of
the calls appear to use ordinary character, numeric, or factor types,
and none performed error catching, so no obvious problems with my
proposed changes stand out.

Furthermore, in looking through the r-help archives, I noted these
messages on r-help where people were having trouble using kruskal.test
and where I think either of my proposed changes would have helped them
perform their desired Kruskal-Wallis rank sum tests.

  <1280836078385-2311712.post at n4.nabble.com>
  <1280849183252-2312063.post at n4.nabble.com>

Conclusions
-----------
I have yet to find any example of my proposed changes causing a
regression. I believe that the most reasonable thing that it might
break is something that depends on either kruskal.test raising an
error or that depends on the specific text in the error message.

If the limited testing is a concern, I could find a way to install
all of the packages and run all of their examples.

Thomas Levine writes:
> I have yet to find any example of my proposed changes causing a
> regression. I believe that the most reasonable thing that it might
> break is something that depends on either kruskal.test raising an
> error or that depends on the specific text in the error message.
>
> If the limited testing is a concern, I could find a way to install
> all of the packages and run all of their examples.
In case my April message is hard to find, I have attached the packages
redundantly to this email.

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>>>>> Thomas Levine writes:
Thanks: this is now fixed in the trunk with c74945.

Best
-k
> I submit a couple options for addressing bug 16719: kruskal.test
> documentation for formula.
> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16719
> disallow-character.diff changes the documentation and error message
> to indicate that factors are accepted.
> allow-character.diff changes the kruskal.test functions to convert
> character vectors to factors; documentation is updated accordingly.
> I tested the updated functions with the examples in example.R. It is
> based on the examples in the bug report.
> If there is interest in applying either patch, especially the latter,
> I want first to test the change on lots of existing programs that call
> kruskal.test, to see if it causes any regressions. Is there a good place
> to look for programs that use particular R functions?
> I am having trouble building R, so I have so far tested these changes
> only by patching revision 74631 (SVN head) and sourcing the resulting
> kruskal.test.R in R 3.4.1 on OpenBSD 6.2. I thus have not tested the
> R documentation files.
> x[DELETED ATTACHMENT disallow-character.diff, plain text]
> x[DELETED ATTACHMENT allow-character.diff, plain text]
> x[DELETED ATTACHMENT example.R, plain text]
> ______________________________________________
> R-devel at r-project.org mailing list
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